Instrument for cassette for sample preparation

ABSTRACT

A parallel preceding system for processing samples is described. In one embodiment, the parallel processing system includes an instrument interface parallel controller to control a tray motor driving system, a close-loop heater control and detection system, a magnetic particle transfer system, a reagent release system, a reagent pre-mix pumping system and a wash buffer pumping system.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.15/006,494 (now U.S. Pat. No. 9,434,939), entitled “Instrument forCassette for Sample Preparation,” filed Jan. 26, 2016 which is acontinuation of U.S. patent application Ser. No. 14/525,976 (now U.S.Pat. No. 9,273,344), entitled “Instrument for Cassette for SamplePreparation,” filed Oct. 28, 2014, which is a continuation of U.S.patent application Ser. No. 13/459,469 (now U.S. Pat. No. 8,900,877),entitled “Instrument for Cassette for Sample Preparation,” filed Apr.30, 2012, which is a continuation U.S. patent application Ser. No.13/234,770 (now U.S. Pat. No. 8,168,443), entitled “Instrument forCassette for Sample Preparation,” filed Sep. 16, 2011, which is acontinuation of U.S. patent application Ser. No. 13/044,109 (now U.S.Pat. No. 8,029,746), entitled “Instrument for Cassette for SamplePreparation,” filed Mar. 9, 2011, which is a continuation of U.S. patentapplication Ser. No. 12/821,446 (now U.S. Pat. No. 7,910,062), entitled“Instrument for Cassette for Sample Preparation,” filed Jun. 23, 2010,which is a continuation of U.S. patent application Ser. No. 12/005,860(now U.S. Pat. No. 7,754,148), entitled “Instrument for Cassette forSample Preparation,” filed Dec. 27, 2007, which claims priority to U.S.Provisional Application Ser. No. 60/882,150, entitled “Instrument forCassette for Sample Preparation,” filed Dec. 27, 2006, each of which isincorporated herein by reference in its entirety.

FIELD

The present invention relates to the field of biotechnology devices and,in particular, to devices and methods for preparing samples.

BACKGROUND

DNA can be used to develop new drugs or to link someone to a crime.However, before this can be done, the DNA must be isolated from asample. These samples include, for example, blood, urine, human cells,hair, bacteria, yeast and tissue. Each of these samples include cells,which include nucleic acid. Nucleic acid is a nucleotide chain, whichconveys genetic information. The most common forms of nucleic acid areDNA and RNA.

In order to isolate the nucleic acid from the samples, prior art devicesuse a tray having several exposed cavities. The sample is placed intoone of the cavities and conventional processing steps are used toisolate the DNA from the sample.

This prior art system has several disadvantages, includingcontamination, and inability to perform parallel processing orasynchronous processing. Since the cavities are exposed, contaminantscan easily affect the DNA. In addition, the prior art system requiresthe preparation of several samples at one time. In addition, these priorart systems require a significant amount of time to process multiplesamples.

SUMMARY

In one embodiment, the present invention relates to an instrument forpreparing samples. The instrument includes, for example, a parallel traymotor driving system; a close-loop heater control and detection system;a parallel magnetic particle transfer system; a parallel reagent releasesystem; a reagent parallel pre-mix pumping system; a parallel washbuffer pumping system; and an instrument interface controller to controlthe biological sample processing instrument that includes the paralleltray motor driving system, the close-loop heater control and detectionsystem, the parallel magnetic particle transfer system, the parallelreagent release system, the parallel reagent pre-mix pumping system, andthe parallel wash buffer pumping system.

In another embodiment, the present invention relates to a system forpreparing samples. The system includes, for example, an enclosure; aparallel tray motor driving system in the enclosure to insert one ormore magazines which contain one or more cassettes into the enclosure,the cassette having a sample therein; a closed-loop heater control anddetection system in the enclosure; a parallel magnetic particle transfersystem in the enclosure; a parallel reagent release system in theenclosure; a parallel reagent pre-mix pumping system in the enclosure;and a parallel wash buffer pumping system in the enclosure.

BRIEF DESCRIPTION OF THE DRAWINGS

The invention is described by way of example with reference to theaccompanying drawings, wherein:

FIG. 1 is a perspective view of an instrument for a cassette for samplepreparation in accordance with one embodiment of the invention;

FIG. 2 is a perspective view of a magazine insertable into theinstrument of FIG. 1 in accordance with one embodiment of the invention;

FIG. 3 is a perspective view of a cassette for preparing samples inaccordance with one embodiment of the invention;

FIG. 4 is a cross-sectional side view of the cassette for preparingsamples of FIG. 3 in accordance with one embodiment of the invention;

FIG. 5 is a perspective view of an instrument for a cassette for samplepreparation in accordance with one embodiment of the invention;

FIG. 6A is a block diagram of the system of the instrument of FIG. 5 inaccordance with one embodiment of the invention;

FIG. 6B is a top level digital block diagram of the system controller ofthe instrument of FIG. 5 in accordance with one embodiment of theinvention;

FIG. 6C is a digital processing block diagram of the system controllerof the instrument of FIG. 5 in accordance with one embodiment of theinvention;

FIG. 6D is an Instrument Module (IM) block diagram of FIG. 5 inaccordance with one embodiment of the invention;

FIG. 7 is a detailed perspective view of a parallel tray driving motorassembly module in accordance with one embodiment of the invention;

FIG. 8 is a detailed perspective view of the reagent release and pre-mixassembly module in accordance with one embodiment of the invention;

FIG. 9 is a detailed side view of the reagent release and pre-mixassembly module in accordance with one embodiment of the invention;

FIG. 10 is a detailed perspective view of a close-loop heater andtemperature sensor assembly module in accordance with one embodiment ofthe invention;

FIG. 11 is a detailed side view of the close-loop heater and temperaturesensor assembly module in accordance with one embodiment of theinvention;

FIG. 12 is a detailed perspective view of a parallel wash buffer pumpingassembly module in accordance with one embodiment of the invention;

FIG. 13 is a detailed side view of the parallel wash buffer pumpingassembly module in accordance with one embodiment of the invention;

FIG. 14 is a detailed perspective view of a parallel magnetic particlestransfer assembly module in accordance with one embodiment of theinvention; and

FIG. 15 is a detailed side view of the parallel magnetic particlestransfer assembly module in accordance with one embodiment of theinvention.

DETAILED DESCRIPTION

FIG. 1 illustrates an instrument 100 in accordance with one embodimentof the invention. In one embodiment, the instrument 100 is a parallelprocessing system.

The illustrated instrument 100 includes a display 104 and openings 108.The openings 108 are configured to receive magazines 120. The magazines120 each contain a series of cassettes 124. Each cassette includes asample of cells to be prepared. A protocol may be selected by a user atthe display 104 for preparing the sample in the cassette 124 within theinstrument 100. The instrument 100 then automatically prepares thesample within the instrument according to the selected protocol.

In the embodiment illustrated in FIG. 1, the instrument can process fourmagazines 120, each magazine 120 having twelve cassettes 124, eachcassette having a sample of cells therein at the same time according tothe selected protocol. It will be appreciated, however, that fewer thanforty-eight or greater than forty-eight samples can be processed at atime.

FIG. 2 illustrates a magazine 200 in further detail. In one embodiment,the magazine 200 is the magazine 120 of FIG. 1. In one embodiment, themagazine 200 is a rack. Several cassettes 224 (e.g., cassettes 124 fromFIG. 1) are placed into the magazine 200.

FIG. 3 illustrates a cassette 300 in further detail. In one embodiment,the cassette 300 is the cassettes 124 in FIG. 1 and/or cassettes 224 inFIG. 2. The cassette 300 can be used to prepare cell samples.

FIG. 4 is a detailed view of the cassette of FIG. 3. The cassette 400includes a housing 412, a mixing chamber 414, first, second, third andfourth holding chambers 416, 418, 420 and 422, first, second, third andfourth plungers 424, 426, 428 and 430, first, second and third valves432, 434 and 436, first and second washing chambers 438 and 440, anelution chamber 442, first, second, third and fourth pumps 444, 446, 448and 450, first and second lids 452 and 454, first and second heatingelements 456 and 458 and a magnetic 460. Each of the chambers 414, 416,418, 420, 422, 438, 440 and 442, plungers 424, 426, 428 and 430, valves432, 434, 436, pumps 444, 446, 448 and 450, and heating elements 456 and458 are enclosed within the housing 412. The lids 452 and 454 aremovably attached to the housing 412. The magnet 460 is removablypositionable in the first valve 432, second valve 434 and third valve436.

The mixing chamber 414 has a top surface 462, a bottom surface 464 andopposing side surfaces 466, 468. The top surface 462 of the mixingchamber 414 includes an opening 470 therein.

The first lid 452 is configured to provide access to the opening 470 inthe top surface 460 of the mixing chamber 414. The first lid 452 and theopening 470 are coaxial. The first lid 452 is shown being movablyattached to the housing 412, such that when the lid 452 is open or off,the opening 470 is accessible and if the lid 452 is closed or on, theopening 470 is not accessible.

A thin film 474 forms one wall of the mixing chamber 414. The thinchamber 474 is breakable, such that the mixing chamber 414 is accessiblewhen the thin film 474 has been broken or ruptured.

The first holding chamber 416, second holding chamber 418, third holdingchamber 420 and fourth holding chamber 422 are shown located next to themixing chamber 414 and aligned vertically with one another. Each of theholding chambers 416, 418, 420, 422 has an opening 476 next to the thinfilm 474 of the mixing chamber 414.

The cassette 400 further includes magnetic iron particles in the form ofmagnetic beads in the first holding chamber 416. The cassette 400further includes a binding solution in the second holding chamber 418.The cassette 400 further includes a lysis solution in the third holdingchamber 420. The cassette 400 further includes a proteinase K (PK)solution in the fourth holding chamber 422. The magnetic iron particles(in the form of magnetic beads), lysis solution, binding solution, andproteinase K (PK) can also be provided in any chamber of the cassette400 based on desired protocol.

The first, second, third and fourth plungers 424, 426, 428 and 430 arelocated in the first, second, third and fourth holding chambers 416,418, 420 and 422, respectively.

Each of the plungers 416, 418, 420, 422 includes a base 478, a shaft 480and a piercing element 482. The shaft 480 extends from the base 478. Thepiercing element 482 is at the end of the shaft 480 opposing the base478 and is pointed. The piercing element 482 is configured to break orrupture the thin film 474 of the mixing chamber 414.

The first pump 444 is a bellows pump having a pumping portion and anozzle portion. The nozzle portion of the first pump 444 is locatedinside the mixing chamber 414. The pumping portion of the first pump 444is located outside the mixing chamber, such that the pumping portion isactuatable.

A heating element 456 is provided at the bottom surface 464 of themixing chamber 414 for heating the contents of the mixing chamber 414.The heating element 456 may be a variable heating element.

The opposing side surface 468 of the mixing chamber 414 also includes anopening 484. A first valve 432 is provided between the opening 484 inthe side 468 of the mixing chamber 414 and the first washing chamber438.

The first valve 432 has a first stationary piece 486 and a secondmoveable piece 488, the second piece 488 being moveable relative to thefirst piece 486. The first stationary piece 486 includes a first opening490 and a second opening 492 and has a surface 494. The second piece 488has an opening 495 therein for receiving the magnet 460. The secondpiece 488 has a surface 496 with a cavity 498 therein. The magnet 460 isshaped to correspond to the opening 495 in the second piece 488. Themagnet 460 is moveable in the opening 495 of the second piece 488, andis removable from the second piece 488.

The cassette 400 includes a washing solution in the first washingchamber 438. The second pump 446 is also a bellows pump, and the nozzleportion of the second pump 446 is located in the first washing chamber438.

The second valve 434 is provided between the first washing chamber 438and the second washing chamber 440. The second valve 434 is structurallyand functionally the same as the first valve 432, and also includes afirst stationary piece 486 and a second moveable piece 488. The firststationary piece 486 includes a first opening 490 and a second opening492 and has a surface 494. The second moveable piece has a surface 496with a cavity 498 therein.

The cassette 400 includes a washing solution in the second washingchamber 440. The third pump 448 is also a bellows pump, and the nozzleportion of the third pump 448 is located in the second washing chamber440.

The third valve 436 is provided between the second washing chamber 440and the elution chamber 442. The third valve 436 is structurally andfunctionally the same as the first valve 432, and also includes a firststationary piece 486 and a second moveable piece 488. The firststationary piece 486 includes a first opening 490 and a second opening492 and has a surface 494. The second moveable piece has a surface 496with a cavity 498 therein.

The cassette 400 includes a washing solution in the elution chamber 442.The fourth pump 450 is also a bellows pump, and the nozzle portion ofthe fourth pump 450 is located in the elution chamber 442.

A heating element 458 is provided at the bottom surface of the elutionchamber 442 for heating the contents of the elution chamber 442. Theheating element 458 may be a variable heating element.

The elution chamber 442 includes an opening 499 at its top surface foraccessing the contents of the elution chamber 442.

The second lid 442 is configured to provide access to the opening 499 inthe top surface of the elution chamber 442. The second lid 454 iscoaxial with the opening 499. The second lid 454 is shown being movablyattached to the housing 412, such that when the lid 454 is open or off,the opening 499 is accessible and if the lid 454 is closed or on, theopening 499 is not accessible.

In use, the first lid 452 is removed to provide access to the opening470 of the mixing chamber 414. A sample of cells is placed into thecassette 400 and, in particular, into the mixing chamber 414. The cellsin the sample include nucleic acid.

The PK solution is then added to the sample. The PK solution is added bymoving the plunger 430 in the fourth holding chamber 422. A force isapplied to the base 478 of the plunger 430 to move the plunger 430. Asthe piercing element 482 of the plunger 430 advances toward the mixingchamber 414, the piercing element 482 punctures and ruptures the thinfilm 474. The break in the thin film 474 provides access to the mixingchamber 414. Continued motion of the plunger 430 transfers the contents(e.g., PK solution) of the first holding chamber 422 into the mixingchamber 414.

The PK solution is mixed with the sample by pumping the mixture with,for example, the first pump 444. The PK solution breaks up/destroys thewalls of the cells of the sample, creating bulk material and nucleicacid in the bulk material.

The lysis solution is then added to the sample in a manner similar tothe PK solution. The lysis solution is typically a salt or detergent.The lysis solution is used to solubilize the bulk material. The lysissolution typically does not solubilize proteins.

The heating element 456 may be used to heat the lysis solution andsample. As described hereinabove, the temperature of the heating element456 may be variable, and is selected to optimize the effectiveness ofthe lysis solution.

The binding solution is then added to the sample, PK solution and lysisbuffer solution. The binding solution is typically hydrophobic andincreases salt in the solution. The binding solution causes the nucleicacid to be magnetically charged.

The magnetic beads are then added to the solution and pumped. Themagnetic beads bind to the magnetically charged nucleic acid.

The magnetic beads, together with the nucleic acid, are bound to thefirst valve 432. The removable positionable magnet 460 is placed in thefirst valve 432 and slid to a position in the first valve 432 to attractthe magnetic beads, which are bound to the nucleic acid, from the mixingchamber 414 to the first valve 432.

The magnetic beads, together with the nucleic acid, are then moved fromthe mixing chamber 414 and received in the first washing chamber 438.

The magnet 460 is inserted into the opening 494 of the second piece 488.The magnet 460 is inserted to a position corresponding to the openings490 and 492 of the first piece 486. The magnet 460 attracts the magneticbeads from the mixing chamber 414 through the opening 490 in the firstpiece 486 and into the cavity 498 in the second piece 488. The secondpiece 488 is rotated such that the magnetic beads are scaled in thecavity 498 of the second piece 488, between surfaces of the second piece488 and the first piece 486. The second piece 488 is rotated past thesurface 494 of the first piece 486, such that the cavity 498 isaccessible in the opening 492 of the first piece 486. The magnet 460 isthen removed from the opening 494 in the second piece 488 to release themagnetic beads from the cavity 498 in the second piece 488.

The magnetic beads and nucleic acid are then washed with the washingsolution by pumping the solution with the second pump 446. The magneticbeads, together with the nucleic acid, are then bound to the secondvalve 434 by inserting the magnet 460 into the second valve 434.

The magnetic beads, together with the nucleic acid, are then moved fromthe first washing chamber 438 to the second washing chamber 440 usingthe second valve 434. The second valve 434 transfers the magnetic beadsand nucleic acid from the first washing chamber 438 to the secondwashing chamber 440.

The magnetic beads and nucleic acid are then washed with the washingsolution a second time by pumping the solution with the third pump 448.The magnetic beads, together with the nucleic acid, are then bound tothe third valve 436 by positioning the magnet 460 in the third valve436.

The magnetic beads and nucleic acid are then moved from the secondwashing chamber 440 to the elution chamber 442. The magnetic beads andnucleic acid are transferred from the second washing chamber 440 to theelution chamber 442.

An elution buffer solution is then mixed with the magnetic beads andnucleic acid by pumping the solution with the fourth pump 450. Theheating element 458 may be used to heat the elution buffer, magneticbeads and nucleic acid. The temperature may be variable and may beselected to optimize release of the nucleic acid from the magneticbeads.

The magnetic beads alone are then bound again to the third valve 436 bypositioning the magnet 460 in the third valve 436.

The magnetic beads alone are then moved from the elution chamber 442back into the second washing chamber 440, leaving the nucleic acid inthe elution chamber 442. The magnetic beads are transferred from theelution chamber 442 to the second washing chamber 440.

The prepared sample of nucleic acid may be accessed from the opening 499in the elution chamber 442. The second lid 54 is removed to provideaccess to the opening 499 in the elution chamber 42.

In one embodiment, a pipette or a multi-channel pipette may be used toplace the sample in the cassette and/or access the sample or a pluralityof samples in the cassette(s).

It will be appreciated that the cassette may vary from that illustratedand described above. For example, seals may be provided in the cassetteas need. In another example, although the cassette 400 has beendescribed as having a mixing chamber 414, two washing chambers 438 and440 and an elution chamber 442, it is envisioned that only one washingchamber or no washing chamber may alternatively be provided.

In another example, the valves may have a different arrangement thanthat described above. In another example, although the cassette has beendescribed as using a single removable magnet 460, it is envisioned thateach valve may include a positionable magnet, such that the magnet doesnot need to be removed. The magnet 460 may be rotatable, and used torotate the second piece of the valves. Alternatively, the magnet mayonly slide inside of each of the valves, and the second piece is rotatedindependent of the magnet. It is envisioned that a cassette 400 thatdoes not use valves as described herein may be used to transfer themagnetic particles from the mixing chamber to the elution chamber. Insuch an embodiment, a slideable magnet may be provided to transfer themagnetic particles from one chamber to the next.

It is envisioned that the housing 412 may be transparent, such that theprocedure can be viewed. In one embodiment the thin film 474 is alamination. In one embodiment, the lids 452 and 454 may be screw-toplids. In one embodiment, the lids 452, 454 include a hydrophobicmembrane, which allows gasses to vent through the lid, but does notallow the liquids to escape the cassette 400. In one embodiment, pump450 is insertable into opening 499. In one embodiment, pump 450 can alsobe used as a pipette to remove the sample from the cassette 400. It isalso envisioned that the mixing chamber 414 may be provided without apuncturable thin film 474. In such an embodiment, the plungers 424, 426,428 and 430 would not need a piercing element 482. Instead, the plungers424, 426, 428 and 430 would have a sealing element to prevent leakage ofthe contents of the holding chamber 416, 418, 420 and 422, associatedwith each plunger 424, 426, 428 and 430, respectively, until the plungerwas moved.

In one embodiment, a total of about 200 μL sample is placed into thecassette. The sample is mixed with a total of about 50 μL of the PKsolution by pumping the mixture of the sample and PK solution for aboutone minute. A total of about 200 μL of the lysis solution is added tothe sample and PK solution, and the solutions are pumped for about oneminute to mix the solutions. The mixture is then heated at about 60° C.for about ten minutes, and the mixture is allowed to cool for about 5minutes. The mixture is further pumped while it cools. A total of about500 μL of binding solution is added to the mixture. The solutions arepumped for about one minute. The magnetic beads are added to thesolution and pumped for about two minutes. The magnetic beads aretransferred and washed as described above. A total of about 700 μL ofwashing solution is provided in each of the washing chambers. A total ofabout 200 μL of elution solution is provided in the elution chamber. Themagnetic beads are mixed with the elution solution by pumping themixture for about one minute. The mixture is then heated at about 90° C.for about two minutes. The process continues as previously described. Itwill be appreciated that the amounts, times and temperatures describedabove may vary from that described above.

Although the cassette 400 has been described as using a PK solution,lysis solution, binding solution and magnetic beads to release thenucleic acid and magnetic beads, it is envisioned that it may bepossible to practice the invention without using each of the abovesolutions. In addition, although the solution was described as using aPK solution to break up the cells, it is envisioned that any enzymewhich causes cells to break up to release nucleic acid may be used withthe invention. Furthermore, it will be appreciated that additionalsolutions may be provided, as needed, to prepare the sample. One ofskill in the art will also understand that the cassette 400 may bemodified to have fewer holding chambers if fewer solutions are used oradditional holding chambers if additional solutions are used.

FIG. 5 illustrates another embodiment of an instrument 500 in accordancewith one embodiment of the invention. It will be appreciated that themagazine and cassettes described herein with reference to FIGS. 2-4 canbe used with the instrument 500. The instrument 500 allows for parallelprocessing of one or more samples within a closed, sterile environment.

Instrument 500 includes an enclosure 502, an instrument handle 504,stackable holders 506, an instrument module 508, a computer module 510,a touch panel display 512, an instrument run time indicator 514, firstand second automatic eject/load trays 516, 518, first and second traydoors 520, 522, and first and second tray safety guards 524, 526.

The instrument module 508 is within the enclosure 502 and is configuredto perform the protocol selected to prepare the sample. The protocol isselected by the user using the touch screen display 512. In oneembodiment, the display 512 is a touch screen display. For example, thedisplay 512 may be, for example, a 7″ to 12″ touch screen LCD display.The user's selection at the display 512 is communicated to the computermodule 510 which communicates with the instrument module 508 via acontroller area network bus (CAN-BUS) to coordinate processing withinthe instrument 500.

The stackable holders 506 enable multiple instruments 500 to be stackedon top of one another such that even more samples can be processed atany given time. In one embodiment, one computer module 510 and display512 may be provided to control processing within multiple stackedinstruments.

The first and second automatic eject/load trays 516, 518 are configuredto receive a magazine (e.g., magazine 200) having one or more cassettestherein (e.g., cassette 400). The magazines are automatically loadedinto the instrument 500 by the automatic eject/load trays 516, 518. Thefirst and second cassette doors 520, 522 are closed and engage with thefirst and second tray safety guards 524, 526 to secure the magazine andcassettes within the enclosure 502 of the instrument 500 for preparationof the sample. It will be appreciated that in alternative embodimentsthe trays 516, 518 and/or doors 520, 522 may be manually opened andclosed.

In one embodiment, the instrument run time indicator 514 is an LED orother exemplary light source. The instrument run time indicator 514 isilluminated to indicate to a user about the instrument ID and runstatus. In one embodiment, the computer module 510 provides anindication to the instrument run time indicator 514 to illuminate thecommunication status between the controller and the instrument.

FIG. 6A is a block diagram of the system components 600 of theinstrument 500. The system components 600 include, a main computer 602,a display panel 604, a sub-system computer 606, an instrument interfaceparallel controller 608, an instrument real time microcontroller unit(MCU) 610, a cooling system 612, a tray motor driving system 614, aheater control and detection system 616, a magnetic particle transfersystem 618, a reagent release system 620, a reagent pre-mix pumpingsystem 622 and a wash buffer pumping system 624.

Each of the cooling system 612, tray motor driving system 614, heatercontrol and detection system 616, magnetic particle transfer system 618,reagent release system 620, reagent pre-mix pumping system 622 and washbuffer pumping system 624 communicate with the instrument interfaceparallel controller 608. In one embodiment, the instrument interfaceparallel controller is configured to control the subsystems 612-624 suchthat up to twenty-four samples can be prepared at a given time. It willbe appreciated, however, that the instrument can be configured toprepare fewer than or greater than twenty-four samples. It will beappreciated that the system components 600 communicate with one anotherto enable parallel processing of the sample(s) within the instrument500.

The instrument interface parallel controller 608 also communicates withthe instrument real time MCU 610, the cooling system 612 and thesub-system computer 606. The sub-system computer 606 communicates withthe main computer 602. The main computer 602 communicates with the touchscreen display panel 604.

In one embodiment, the main computer 602, sub-system computer 606,and/or the instrument interface parallel controller 608 are a digitalprocessing system. The digital processing system may include amicroprocessor, an ASIC (application specific integrated circuit), FPGA(field-programmable gate array), DSP (digital signal processor), or thelike. In one embodiment, the display panel 604 is a 7″ high definition(HD) liquid crystal display (LCD) with a touch panel. The display panel604 is on an external surface of the instrument 500 such that the usercan interact with the display panel 604. The main computer 602 may be astand alone system that includes the computer module 510 and display512. The sub-system computer 606 and instrument interface parallelcontroller 608 are within the enclosure 502 of the instrument 500. Asdescribed above with reference to FIG. 5, the user can select a protocolfor processing the sample(s) with the display panel 604. The displaypanel 604 communicates the user selection to the main computer 602,sub-system computer 606 and/or parallel controller 608 to perform theprotocol using the tray motor driving system 614, heater control anddetection system 616, magnetic particle transfer system 618, reagentrelease system 620, reagent pre-mix pumping system 622 and wash bufferpumping system 624.

In one embodiment, the tray motor driving system 614 is configured tocontrol the automatic load/eject trays 516, 518 (from FIG. 5) andcassette doors 520, 522 to automatically load the cassettes (e.g.,cassette 400) for processing and eject the cassettes when processing ofthe sample is completed.

In one embodiment, the heater control and detection system 616 isconfigured to control and detect the temperature of the cassette orcassettes. The heater control and detection system may also control theheaters within the cassette to perform a close loop temperature rampingand detection. Alternatively or in addition to controlling the heaterswithin the cassette, the heater control and detection system 614 mayinclude heaters that are configured as a programmable temperaturecontroller to heat the contents of the cassette to a predefinedtemperature, as needed, according to the selected protocol.

In one embodiment, the magnetic particle transfer system 618 isconfigured to transfer magnetic particles within the cassette (e.g.,cassette 400) according to the selected protocol. In one embodiment, themagnetic particle transfer system 618 manipulates the valves 432, 434,436 to transfer the magnetic particles as described above with referenceto FIG. 4.

In one embodiment, the reagent release system 620 is configured torelease the reagents within the cassette. For example, the reagentrelease system is configured to release the PK solution, lysis solution,binding solution and magnetic beads from their respective holdingchambers 416, 418, 420 and 422 and into the mixing chamber 414, asdescribed above with reference to FIG. 4.

In one embodiment, the reagent pre-mix pumping system 622 is configuredto mix the reagents in the mixing chamber 414 as described above withreference to FIG. 4.

In one embodiment, the wash buffer pumping system 624 is configured topump the washing solution in the cassette, as described above withreference to FIG. 4. For example, the wash buffer pumping system 624 maybe configured to actuate the pumps 446, 448, 450 in the wash chambers438, 440 and elution chamber 442.

FIG. 6B illustrates a block diagram of a digital system 630 inaccordance with one embodiment of the invention. The illustrated digitalsystem 630 includes a system controller module (SCM) 632, a firstinstrument module (IM) 1 634, a second instrument module (IM) 2 636 anda nth instrument module (IM) N 638. The SCM 632 controls each of the IM1 634, IM 2 636 and up to an nth IM N 638. It will be appreciated thatthe SCM 632 may control any number of IMs as represented by N. Thus, Nmay be any number from 0 up to 100 or even more.

FIG. 6C is a block diagram illustrating the system controller module 632of FIG. 6B in further detail. The system controller module 632 includesa main processor unit 640, a Complex Programmable Logic Device (CPLD)642, a Liquid Crystal Display (LCD) 644, a Synchronous Dynamic RandomAccess Memory (SDRAM) 646, a NOR flash 648, a NAND flash 650, a StorageDevice (SD) card 652, a Universal Asynchronous Receiver-Transmitter(UART) 654, a CANBUS 656, a Universal Serial Bus (USB) 658, an Ethernet660 and a system bus 662 to couple each of the components 640-662.

The bus 662 or other internal communication means is for communicatinginformation, and the main processor unit 640 is coupled to the bus 662for processing information. SDRAM 646, NOR flash 648, NAND flash 650,and SD card 652 (referred to as memory) are for storing information andinstructions to be executed by the main processor unit 640, for storingtemporary variables or other intermediate information during executionof instructions by main processor unit 640, for storing staticinformation and instructions for main processor unit 640, and the like.

The system may further be coupled to a display device, such as a cathoderay tube (CRT) or a liquid crystal display (LCD) 644, coupled to bus 662through bus 662 for displaying information to a computer user. Analphanumeric input device 675, including alphanumeric and other keys,may also be coupled to bus 662 through bus 662 for communicatinginformation and command selections to the main processor unit 640. Anadditional user input device is cursor control device, such us a mouse,a trackball, stylus, or cursor direction keys coupled to bus 662 throughbus 662 for communicating direction information and command selectionsto main processor unit 640, and for controlling cursor movement ondisplay device 644.

Another device, which may optionally be coupled to computer system, is acommunication device, such as UART 654, CANBUS 656, USB 658, andEthernet 660, for accessing other nodes of a distributed system via anetwork. The communication device may include any of a number ofcommercially available networking peripheral devices such as those usedfor coupling to an Ethernet, token ring, Internet, control area network(CAN), wide area network (WAN), and wireless network (WIFI). Thecommunication device may further be a null-modem connection via UART, orany other mechanism that provides connectivity between the computersystem and the outside world, or any other mechanism that providesconnectivity between the controller computer system and instrumentmodules. Note that any or all of the components of this systemillustrated in FIG. 6C and associated hardware may be used in variousembodiments of the present invention.

It will be appreciated by those of ordinary skill in the art that anyconfiguration of the system may be used for various purposes accordingto the particular implementation. The control logic or softwareimplementing the present invention can be stored in SDRAM 646, NOR Flash648, HAND flash 650, SD card 652, FPGA, CPLD or other storage mediumlocally or remotely accessible to main processor unit 640.

It will be apparent to those of ordinary skill in the art that thesystem, method, and process described herein can be implemented assoftware stored in memory and executed by main processor unit 640. Thiscontrol logic or software may also be resident on an article ofmanufacture comprising a computer readable medium having computerreadable program code embodied therein and being readable by the storagedevice and for causing the main processor unit 640 to operate inaccordance with the methods and teachings herein.

The present invention may also be embodied in a handheld or portabledevice containing a subset of the computer hardware components describedabove. For example, the handheld device may be configured to containonly the bus 662, the main processor unit 640, and SDRAM 646. Thehandheld device may also be configured to include a set of buttons orinput signaling components with which a user may select from a set ofavailable options. The handheld device may also be configured to includean output apparatus such as a liquid crystal display (LCD) or displayelement matrix for displaying information to a user of the handhelddevice. Conventional methods may be used to implement such a handhelddevice. The implementation of the present invention for such a devicewould be apparent to one of ordinary skill in the art given thedisclosure of the present invention as provided herein.

The present invention may also be embodied in a special purposeappliance including a subset of the computer hardware componentsdescribed above. For example, the appliance may include a main processorunit 640, SDRAM 646 and bus 662, and only rudimentary communicationsmechanisms, such as a small touch-screen that permits the user tocommunicate in a basic manner with the device. In general, the morespecial-purpose the device is, the fewer of the elements need to bepresented for the device to function. In some devices, communicationswith the user may be through a touch-based screen, USB devices, orsimilar mechanism.

It will be appreciated by those of ordinary skill in the art that anyconfiguration of the system may be used for various purposes accordingto the particular implementation. The control logic or softwareimplementing the present invention can be stored on any machine-readablemedium locally or remotely accessible to processor. A machine-readablemedium includes any mechanism for storing or transmitting information ina form readable by a machine (e.g. a computer). For example, a machinereadable medium includes read-only memory (ROM), random access memory(RAM), magnetic disk storage media, optical storage media, flash memorydevices, electrical, optical, acoustical or other forms of propagatedsignals (e.g. carrier waves, infrared signals, digital signals, etc.).

FIG. 6D is a block diagram illustrating the instrument modules 634, 636,638 of FIG. 6B in further detail. The instrument modules 634, 636, 638include a databus 664, a stepper motor controller 666, initial data 667,a main stepper controller 668, an ADC reader 670, an input data device672 and an output data device 674. The stepper motor controller 666,initial data 666, main stepper controller 668, Analog-to-DigitalConverter (ADC) reader 670, input data device 672 and output data device674 are each coupled to the databus 664.

In the embodiment illustrated in FIG. 6D, the instrument module is shownfor the tray motor driving module of FIG. 6A. It will be appreciatedthat the instrument modules for the other modules of FIG. 6A will havesimilar components as the illustrated instrument module; however, theinputs and outputs coupled with the instrument modules may vary.

The illustrated databus 664 is also coupled with a MCU 676. The steppermotor controller 666 is also coupled with the motor sensor 678, motordriver 2 680 and motor driver 3 682. The main stepper controller 668 isalso coupled with the motor driver 1 684 and protect sensor 686. The ADCreader 670 is also coupled with the ADC 688. The input data device 672is also coupled with the door sensor 690, main motor home sensor 692,and cassette sensor 694. The output data device 674 is also coupled withthe fan 696 and the heater 698.

FIG. 7 illustrates a tray driving motor assembly module 700. In oneembodiment, the tray driving motor assembly module 700 is part of thetray motor driving system 614 of FIG. 6. In one embodiment, the traydriving motor assembly module 700 is within the instrument module 508 ofthe instrument 500 as described above with reference to FIG. 5.

The tray driving motor assembly module 700 includes an alignment plate702, a first drive shaft retention block 704, a second drive shaftretention block 706, a load driving shaft 708, a main driving motor 710,a first parallel shaft 712, a second parallel shaft 714, a firstparallel linear drive 716, a second parallel linear drive 718, a firstload resistance tray 720, a first door 722, a second load resistancetray 724 and a second door 726.

The main drive motor 710 is coupled with the load driving shaft 708 viathe retention blocks 704, 706 to automatically load and eject the racktrays 720, 724 into the instrument. The trays 720, 724 also slide alongthe parallel shafts 712, 714 with the main drive motor 710 and thedrives 716, 718 to load and eject the racks 720, 724. The motor 710and/or drivers 712, 714 can also be used to open and close the doors722, 726.

FIG. 8 illustrates a reagent release and pre-mix assembly module 800. Inone embodiment, the reagent release and pre-mix assembly module 800 ispart of the reagent release system 620 and reagent pre-mix pumpingsystem 622. In one embodiment, the reagent release and pre-mix assemblymodule 800 is within the instrument module 508 of the instrument 500 asdescribed above with reference to FIG. 5.

The reagent release and pre-mix assembly module 800 includes a precisionvertical engagement driving motor 802, a vertical drive shaft 803, astand 804, a first plunger assembly 806, a second plunger assembly 808,a first parallel horizontal pump activation motor 810, a second parallelhorizontal pump activation motor 812, first, second, third and fourthhorizontal parallel linear driving shafts and hearings 814, 816, 818 and820, and first, second, third and fourth vertical parallel linearbearings 822, 824, 826 and 828.

In one particular embodiment, each of the plunger assemblies 806, 808includes twelve plungers (e.g., one plunger for each cassette in themagazine). It will be appreciated that the plunger assemblies 806, 808may have fewer than or greater than twelve plungers.

FIG. 9 is a side view of reagent release and pre-mix assembly module 800of FIG. 8. As shown in FIG. 9, the reagent release and pre-mix assemblymodule 800 of FIG. 8 also includes a vertical position sensor 830.

With reference to FIGS. 8 and 9, the stand 804 is coupled with thevertical drive shaft 803, which is coupled with the vertical engagementdriving motor 802 to vertically position the stand 804. The plungerassemblies 806, 808 are coupled with the stand 804 and are, thus, alsovertically positioned with the stand 804 when the motor 802 is actuated.The vertical position sensor 830 is coupled with the stand 804 to sensethe position of the stand 804 and/or plunger assemblies 806, 808. Thevertical position sensor 830 communicates with a controller to controlactuation of the motor 802. The plunger assemblies 806, 808 are alsoactuatable horizontally via the horizontal drive shafts and bearings814-820, which are coupled with the horizontal motors 810, 812.

The plunger assemblies 806, 808 are actuated in a vertical direction toalign the plungers 806, 808 with one of the holding chambers of thecassette 400. The plunger assemblies 806, 808 are also actuatedhorizontally to force the contents of the holding chambers into themixing chamber of the cassette 400. The plunger assemblies 806, 808 arethen repositioned vertically to align with another holding chamber andare similarly actuated horizontally to force the contents of the holdingchamber into the mixing chamber according to the selected protocol. Inone embodiment, the plunger assemblies 806, 808 are also actuated toactuate the pump 444 that mixes the contents of the mixing chamber ofthe cassette 400.

FIGS. 10 and 11 illustrate a heater and temperature sensor assemblymodule 1000. In one embodiment, the heater and temperature sensorassembly module 1000 is part of the heater control and detection system616. In one embodiment, the heater and temperature sensor assemblymodule 1000 is within the instrument module 508 of the instrument 500 asdescribed above with reference to FIG. 5.

The heater and temperature sensor assembly module 1000 includes aprecision vertical engagement driving motor 1002, a vertical positionsensor 1004, a rack 1006, a first vertical linear bearing 1008, a secondvertical linear bearing 1010, a plurality of heater and thermal sensorconnectors 1012 and a plurality of individually controlled parallelheaters and thermal sensors 1014. In one embodiment, the plurality ofindividually controlled parallel heaters and thermal sensors 1014 areself-aligned with the plurality of heater and thermal sensor connectors1012.

In one particular embodiment, the heater and temperature sensor assemblymodule 1000 includes twenty-four heater and thermal sensor connectors1012 and twenty-four individually controlled parallel heaters andthermal sensors 1014. It will be appreciated that the heater andtemperature sensor assembly module 1000 may include fewer than orgreater than twenty-four connectors 1012 and/or heaters/sensors 1014.

The vertical linear bearings 1008, 1010 are coupled with the verticalengagement driving motor 1002 to vertically position the rack 1006. Theplurality of heater and thermal sensor connectors 1012 and plurality ofindividually controlled parallel heaters and thermal sensors 1014 arecoupled with respective sides of the rack 1006. The plurality of heaterand thermal sensor connectors 1012 and plurality of individuallycontrolled parallel heaters and thermal sensors 1014 are verticallypositionable by vertically positioning the rack 1006. The verticalprecision position sensor 1004, coupled with the rack 1006, can be usedto accurately position the plurality of heater and thermal sensorconnectors 1012 and plurality of individually controlled parallelheaters and thermal sensors 1014.

FIGS. 12 and 13 illustrate a wash buffer pumping assembly module 1200.In one embodiment, the wash buffer pumping assembly module 1200 is partof the wash buffer pumping system 624. In one embodiment, the washbuffer pumping assembly module 1200 is within the instrument module 508of the instrument 500 as described above with reference to FIG. 5.

The wash buffer pumping assembly module 1200 includes a rack 1202, aplurality of parallel vertical pump engagement plungers 1204, a firstparallel vertical pump activation motor 1206, a second parallel verticalpump activation motor 1208, and first, second, third and fourth verticalparallel linear driving shafts and bearings 1210, 1212, 1214 and 1216.As shown in FIG. 13, the wash buffer pumping assembly module 1200 alsoincludes first and second vertical precision position sensors 1218 and1220.

The first vertical pump activation motor 1206 is coupled with the firstand second vertical parallel linear driving shafts and bearings 1210,1212 to vertically position a first set of parallel vertical pumpengagement plungers 1204 a. Similarly, the second vertical pumpactivation motor 1206 is coupled with the third and fourth verticalparallel linear driving shafts and bearings 1214, 1216 to verticallyposition a second set of parallel vertical pump engagement plungers 1204b.

The plungers from the vertical pump engagement plungers 1204 engage withthe cassette (e.g., cassette 400) to actuate the pumps 446, 448, 450 inthe wash chambers 438, 440 and elution chamber 442 according to theselected protocol.

FIGS. 14 and 15 illustrate a magnetic particles transfer assembly module1400. In one embodiment, the magnetic particles transfer assembly module1400 is part of the magnetic panicle transfer system 618. In oneembodiment, the magnetic particles transfer assembly module 1400 iswithin the instrument module 508 of the instrument 500 as describedabove with reference to FIG. 5.

The magnetic particles transfer assembly module 1400 includes a rack1402, a precision vertical engagement driving motor 1402, a firstparticle transfer linear motor 1404, a second particle transfer linearmotor 1406, first, second, third and fourth gear rack retention rollerbearings 1408, 1410, 1412 and 1416, first and second vertical linearbearings 1418 and 1420, first and second driving gear racks 1422, 1423,a plurality of parallel precision gears 1424 and a plurality of parallelmagnets and valve key shafts 1426. As shown in FIG. 15, the magneticparticles transfer assembly module 1400 also includes first and secondlinear driving shafts 1428 and 1430, first, second, third and fourthshaft and gear rack link blocks 1432, 1434, 1436 and 1438, first,second, third and fourth horizontal precision position sensors 1440,1442, 1444 and 1446, and a vertical precision position sensor 1448.

In one particular embodiment, the magnetic particles transfer assemblymodule 1400 includes twenty-four parallel precision gears 1424 andtwenty-four parallel magnets and valve key shafts 1426. It will beappreciated that the magnetic particles transfer assembly module 1400may have fewer than or greater than twenty-four gears 1424 and magnetsand key shafts 1426.

The precision vertical engagement driving motor 1402 is coupled withvertical bearings 1418, 1420 and the rack 1403 to vertically positionthe rack 1403. The plurality of parallel magnets and valve key shafts1426 are positioned on the rack 1403 and are vertically positioned whenthe rack 1403 is vertically positioned. The vertical precision positionsensor 1448 is coupled with the rack 1403 and motor 1402 to accuratelyposition the plurality of parallel magnets and valve key shafts 1426 inthe cassette (e.g., cassette 400).

The particle transfer linear motors 1404, 1405 are positioned on eitherend of the rack 1403 and are coupled with the linear driving shafts1428, 1430, shaft and gear rack link blocks 1432-1438, driving gearracks 1422, gears 1424, to horizontally position and rotate theplurality of parallel magnets and valve key shafts 1426 via the gears1424 to transfer magnetic particles as described above with reference toFIG. 4. It will be appreciated that the gears 1424 and magnets andshafts 1426 can be repositioned to transfer the panicles with each valveof the cassette.

The foregoing description with attached drawings is only illustrative ofpossible embodiments of the described method and should only beconstrued as such. Other persons of ordinary skill in the art willrealize that many other specific embodiments are possible that fallwithin the scope and spirit of the present idea. The scope of theinvention is indicated by the following claims rather than by theforegoing description. Any and all modifications which come within themeaning and range of equivalency of the following claims are to beconsidered within their scope.

The invention claimed is:
 1. A system comprising: a plurality ofstackable enclosures stacked one on top of the other, wherein eachstackable enclosure of the plurality of stackable enclosures comprises:(i) at least one opening configured to receive one or more cassettes,(ii) at least one actuator assembly, said actuator assembly comprising aplurality of plungers configured to be movable between a first positionand a second position such that the plurality of plungers are configuredto engage a surface of the one or more cassettes when the plurality ofplungers are moved from the first position to the second position; and(iii) at least one sub-system computer; a system controller modulecomprising a single, touch-panel display and a main computer configuredto communicate with the single, touch-panel display and the sub-systemcomputer in the plurality of stackable enclosures.
 2. The system ofclaim 1 further comprising a cassette disposed within at least one ofthe plurality of stackable enclosures.
 3. The system of claim 2, whereinthe cassette contains a sample of cells.
 4. The system of claim 3,wherein the cassette contains a cell lysis solution.
 5. The system ofclaim 1, wherein the single touch-panel display is a liquid crystaldisplay (LCD).
 6. The system of claim 1, wherein the system furthercomprises a networking peripheral device.
 7. The system of claim 1,wherein each stackable enclosure of the plurality of stackableenclosures has two openings configured to receive one or more cassettes.8. The system of claim 1, further comprising a tray driving motorsystem.
 9. The system of claim 7, wherein each stackable enclosure has afirst opening and a second opening configured to receive one or morecassettes, and further wherein the tray driving motor system comprises:(i) an alignment plate; (ii) a first drive shaft retention block coupledto the alignment plate; (iii) a second drive shaft retention blockcoupled to the alignment plate; (iv) a load driving shaft; (v) a maindriving motor coupled with the load driving shaft via the first driveshaft retention block and the second drive shaft retention block; (vi) afirst parallel shaft; (vii) a second parallel shaft; (viii) a firstparallel linear drive movably coupled to the first parallel shaft, (ix)a second parallel linear drive movably coupled to the second parallelshaft; (x) a first load resistance tray configured to receive the one ormore cassettes; (xi) a first door configured to cover the first opening;(xii) a second load resistance tray configured to receive the one or orecassettes; and (xiii) a second door a second door configured to coverthe second opening.
 10. The system of claim 1 further comprising aheater and temperature sensor assembly, the heater and temperaturesensor assembly comprising a plurality of heaters and temperaturesensors.
 11. The system of claim 1, wherein each stackable enclosure ofthe plurality of stackable enclosures comprises at least two actuatorassemblies, each actuator assembly comprising a plurality of plungersconfigured to be movable between a first position and a second positionsuch that the plurality of plungers are configured to engage a surfaceof the one or more cassettes when the plurality of plungers are movedfrom the first position to the second position.
 12. The system of claim1, wherein the main computer communicates with the sub-system computervia a universal asynchronous receiver-transmitter (UART).
 13. A systemcomprising: a plurality of stackable enclosures stacked one on top ofthe other, wherein each stackable enclosure of the plurality ofstackable enclosures comprises: (i) at least one opening configured toreceive one or more cassettes, (ii) at least on actuator assembly, saidactuator assembly comprising a plurality of plungers configured to bemovable between a first position and a second position such that theplurality of plungers are configured to engage a surface of the one ormore cassettes when the plurality of plungers are moved from the firstposition to the second position; (iii) at least one heater andtemperature sensor assembly; and (iv) at least one sub-system computer;at least one cassette containing a sample of cells disposed within eachstackable enclosure of the plurality of stackable enclosures; and asystem controller module comprising a single display and a main computerconfigured to communicate with the single display and the sub-systemcomputer in the plurality of stackable enclosures.
 14. The system ofclaim 13, wherein the system further comprises a networking peripheraldevice.
 15. The system of claim 13, wherein the main computercommunicates with the sub-system computer via a universal asynchronousreceiver-transmitter (UART).
 16. The system of claim 13, wherein eachstackable enclosure of the plurality of stackable enclosures has twoopenings configured to receive one or more cassettes.
 17. A method forprocessing a sample of cells comprising: adding a sample of cells to acassette containing a lysis solution and a wash buffer; inserting thecassette in one of the plurality of stackable enclosures of the systemof claim 1; and selecting a protocol for processing the sample in thestackable enclosure using the single, touch-panel display of the systemof claim
 1. 18. The method of claim 17 comprising: adding a plurality ofsamples of cells to a plurality of cassettes containing a lysis solutionand a wash buffer; inserting the plurality of cassettes in the pluralityof stackable enclosures of the system of claim 1; and selecting aprotocol for processing the plurality of samples in the plurality ofstackable enclosures using the single, touch-panel display of the systemof claim
 1. 19. The method of claim 17 further comprising inserting thecassette in a magazine prior to inserting the cassette in the stackableenclosure.
 20. The method of claim 18 further comprising inserting theplurality of cassettes in a plurality of magazines prior to insertingthe plurality of cassettes in the plurality of stackable enclosures.